Exploration of the potential energy surface for the conformational interconversion of the amyloid $\beta$ peptide at the fibril end

TL;DR

This study uses density functional theory to explore the energy landscape of amyloid beta peptide conformations at fibril ends, revealing the energetic and structural factors influencing conformational transitions relevant to Alzheimer's disease.

Contribution

It provides a detailed theoretical analysis of the potential energy surface and transition barriers for amyloid beta fibril conformations, highlighting the role of sidechain interactions.

Findings

Twisted conformations are local minima with specific energy profiles.

Fibril-to-twisted transitions are endothermic, involving hydrogen bond and van der Waals interactions.

Certain twisted conformations revert easily to fibrils, others face higher barriers due to steric hindrance.

Abstract

The formation of amyloid fibrils comprising amyloid $\beta$ (A$\beta$) peptides is associated with the pathology of Alzheimer's disease. In this study, we theoretically investigated the A$\beta$ structure at the fibril end using the density functional theory calculation. Several twisted conformations were identified as local minima in which a part of the peptide chain bends upward while the rest remains bound to the lower A$\beta$ monomer. Fibril-to-twisted conformational transition exhibited endothermic behavior, with endothermic energy increasing as more backbone hydrogen bonds were broken. In addition, the loss of van der Waals interaction from the hydrophobic sidechain contributed to endothermicity. The nudged elastic band method was applied to analyze the potential energy surface connecting the fibril and twisted conformations. Comparison of the activation barriers between different twisted conformations revealed that certain twisted conformations returned relatively easily to the fibril conformation, whereas others encountered a higher activation barrier and reverted less readily. Detailed structural analysis revealed that the twisted conformation's propensity to return originates from the local steric hindrance imposed by the sidechain near the torsional axis.